Biology subjects

Tobias, P.

Publications and source records attributed to Tobias, P..

5 recordsLinked to original sources

bioRxiv2026

Global population genomics and pangenome of the clubroot pathogen link clonal expansion and effector diversification to resistance breakdown in canola

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae, threatens Brassica crops worldwide. Novel pathogen virulence frequently breaks resistance in agricultural crops, and yet explanations for isolate evolution remain unknown. We combined whole genome sequencing of 192 isolates from 24 countries with a pangenome analysis of 55 high-quality complete or nearly complete genome assemblies and performed functional effector analyses to investigate potential mechanisms of virulence emergence. Three major phylogenetic clusters were identified, including two highly clonal lineages with contrasting virulence profiles, and a genetically diverse population retaining signatures of recombination. Our findings support a model in which genome-wide purifying selection maintained core genome integrity, while effector genes evolved under less constraint. Despite a compact closed pangenome, we identified chromosome 17 as a major hotspot of single nucleotide and structural variations, transposable elements and expansion of ankyrin repeat effectors. Within the variable chromosome 17, PbAnk2 alleles from virulent and avirulent isolates encoded proteins with distinct predicted structures. PbAnk2 interacted with the Arabidopsis co-chaperone DJC31 in yeast two-hybrid and BiFC assays, whereas co-immunoprecipitation did not detect an interaction for the allele found in isolates that break CRa-mediated resistance, suggesting that allelic variation may alter PbAnk2's association with DJC31. These findings reveal the clonal expansion of virulent isolates and connect it to effector diversification that led to resistance breakdown and establish a genomic framework for pathogen surveillance and durable clubroot resistance.

genomics↗

bioRxiv2026

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained production of Arabica coffee for over 150 years. Here, we present a pseudo-phased, chromosome-level genome resource for H. vastatrix, isolate Hv178a, to guide research into disease management. The Hv178a genome assembly is 665 and 638 Mbp for haplotype A and B respectively, localised to 18 chromosomes. We determined that the genomes are highly repetitive at [~]90%, with a GC content of [~]33%. We present the full annotation of 13,760 and 17,998 protein coding genes, and we predicted 452 and 496 effectors in haplotype A and B respectively. Depth-based comparisons with 11 additional H. vastatrix isolates revealed increased chromosome 17 (chr17) copy number in Hv178a. Validation with qPCR supports a chr17 trisomy in Hv178a absent from the ancestral lineage and potentially explaining the observed change in virulence.

genomics↗

bioRxiv2025

Phylogenomics and effector analysis of Plasmodiophora brassicae genomes unveils a unique and highly divergent clade in Australia

Clubroot, caused by the protist pathogen Plasmodiophora brassicae, is a soilborne disease that leads to significant yield losses in a broad range of brassica crops worldwide. Despite its significant impact on agriculture, genomic and molecular studies of clubroot disease are hindered due to the complex life cycle and the obligate biotrophic nature of the pathogen, which prevents its cultivation in vitro. In addition, several genotypes of P. brassicae are often present as a mixture in a single field sample, making it challenging to resolve high-quality assemblies of individual genomes. Recently, several genomes were assembled for some strains of P. brassicae, however, in-depth genomic analysis of this devastating pathogen remains limited. In this study, we generated complete telomere-to-telomere genome assemblies for three Australian P. brassicae field isolates using PacBio Revio HiFi sequencing combined with chromatin conformation capture technology (Hi-C). Importantly, we could generate two nearly fully phased haplotype genome assemblies from one of the field isolates. Additionally, we sequenced 14 isolates of P. brassicae, sampled from a wide geographical range across Australia using Illumina technology and performed an in-depth global comparative phylogenetic analysis. We revealed that Australian isolates are classified into three different clades, including a highly divergent and unique clade present only in Australia. Comparative analysis showed that the predicted effector profile of the Australian-unique clade is distinct from other clades, further supporting phylogenetic divergence. Altogether, we demonstrate the first haplotype-resolved genome of Australian P. brassicae isolates from a single clubroot field sample, and provide an in-depth phylogenetic analysis of global and Australian isolates. These findings, together with core effector profile analysis, will further advance the research to combat this destructive pathogen.

genomics↗

bioRxiv2025

Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii

Rust diseases on plants are caused by fungi in the order Pucciniales. Typically, rust fungi have narrow host specificity however the pandemic biotype of Austropuccinia psidii has an unusually broad host range causing disease on over 480 myrtaceous species globally. We assembled and analysed a fully phased chromosome-level genome for the pandemic A. psidii and addressed key outstanding questions of its infection biology. Our research revealed a conserved rust fungal karyotype of 18 haploid chromosomes, in line with fungi for distantly related cereal rusts. We observed chromosomal re-assortment between the two nuclei, with one nucleus carrying 19 and the other 17 chromosomes. The synteny of universal single-copy orthologs is mostly maintained with the distantly related rust fungus Puccinia graminis f. sp. tritici. In contrast, nucleotide composition and methylation profiles of A. psidii are distinct compared to rust fungi with smaller genome sizes that have not undergone massive transposable element expansions. Our analysis of mating type loci supports a tetrapolar mating system for A. psidii with a novel finding of expanded numbers of pheromone peptide precursors. We show that infection dynamics of A. psidii are consistent on four different susceptible host species separated by 65 mya of evolution and that transcriptional regulation during infection reveals two distinct waves of gene expression in early and late infection, including allele-specific expression of candidate effectors. Together, these findings enhance the understanding of the genome biology and pathology of A. psidii, while also providing a valuable resource for future research on this serious rust pathogen.

microbiology↗

bioRxiv2025

A phased chromosome-level genome resource for a myrtle rust susceptible Syzygium luehmannii

Syzygium luehmannii is an Australian east coast endemic tree within the family Myrtaceae. Syzygium luehmannii is not known to be highly susceptible to the parasitic fungus causing myrtle rust, Austropuccinia psidii, however infections have been reported in the field, and in controlled inoculations. The capacity for this exotic pathogen to parasitise host trees, suggest that molecular targets are present in susceptible plants. While understanding resistance phenotypes is important for tree breeding and management, determining the key drivers for susceptibility may also provide useful additional research targets to avert infection. While there are several genome resources for plants within the large and globally diverse Syzygium genus, there is no diploid genome assembly (2n = 22), and no genome for S. luehmannii. We assembled the genome for S. luehmannii into the pseudo-phased, 11 chromosome pairs here termed haplotype A (370 Mbp) and B (357 Mbp). We annotated the predicted protein coding genes, and we specifically annotated the nucleotide-binding leucine rich repeat (NLR) type resistance genes as a useful resource for plant:pathogen studies. The high quality of this genome provides a base for studies on myrtle rust resistant and susceptible hosts to understand mechanisms of infection.

genomics↗